Exemplo n.º 1
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    def test_deduce_software(self):
        """Test deducing the ESS software"""
        self.job1.job_type = 'onedmin'
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'onedmin')

        self.job1.job_type = 'orbitals'
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'qchem')

        self.job1.job_type = 'composite'
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'gaussian')

        # test the levels_ess dict from settings
        self.job1.job_type = 'opt'
        self.job1.level = Level(repr={'method': 'm06-2x', 'basis': '6-311g'})
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'qchem')

        self.job1.job_type = 'opt'
        self.job1.level = Level(repr={'method': 'ccsd(t)', 'basis': 'cc-pvtz'})
        self.job1.method = 'ccsd(t)'
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'molpro')

        self.job1.job_type = 'opt'
        self.job1.level = Level(repr={'method': 'wb97xd3', 'basis': '6-311g'})
        self.job1.method = 'wb97xd'
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'terachem')

        self.job1.job_type = 'scan'
        self.job1.level = Level(repr={'method': 'm062x', 'basis': '6-311g'})
        self.job1.method = 'm062x'
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'gaussian')

        # return to original value
        self.job1.level = Level(repr='b3lyp/6-31+g(d)')
        self.job1.method = 'b3lyp'
        self.job1.software = None
        self.job1.deduce_software()
        self.assertEqual(self.job1.software, 'gaussian')
Exemplo n.º 2
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 def test_level(self):
     """Test setting up Level"""
     level_1 = Level(method='b3lyp',
                     basis='def2tzvp',
                     auxiliary_basis='aug-def2-svp',
                     dispersion='gd3bj',
                     software='gaussian')
     self.assertEqual(level_1.method, 'b3lyp')
     self.assertEqual(level_1.basis, 'def2tzvp')
     self.assertEqual(level_1.auxiliary_basis, 'aug-def2-svp')
     self.assertEqual(level_1.dispersion, 'gd3bj')
     self.assertEqual(level_1.software, 'gaussian')
     self.assertEqual(
         str(level_1),
         "b3lyp/def2tzvp, auxiliary_basis: aug-def2-svp, dispersion: gd3bj, software: gaussian (dft)"
     )
     self.assertEqual(level_1.simple(), "b3lyp/def2tzvp")
Exemplo n.º 3
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 def test_build(self):
     """Test bulding a Level object from a string or dict representation"""
     level_1 = Level(repr='wB97xd/def2-tzvp')
     self.assertEqual(level_1.method, 'wb97xd')
     self.assertEqual(level_1.basis, 'def2-tzvp')
     self.assertEqual(level_1.method_type, 'dft')
     self.assertEqual(str(level_1),
                      'wb97xd/def2-tzvp, software: gaussian (dft)')
     level_2 = Level(repr='CBS-QB3')
     self.assertEqual(level_2.method, 'cbs-qb3')
     self.assertIsNone(level_2.basis)
     self.assertEqual(level_2.software, 'gaussian')
     self.assertEqual(level_2.method_type, 'composite')
     self.assertEqual(str(level_2),
                      'cbs-qb3, software: gaussian (composite)')
     self.assertEqual(level_2.simple(), 'cbs-qb3')
     level_3 = Level(
         repr={
             'method': 'DLPNO-CCSD(T)',
             'basis': 'def2-TZVp',
             'auxiliary_basis': 'def2-tzvp/c',
             'solvation_method': 'SMD',
             'solvent': 'water',
             'solvation_scheme_level': 'APFD/def2-TZVp'
         })
     self.assertEqual(level_3.method, 'dlpno-ccsd(t)')
     self.assertEqual(level_3.basis, 'def2-tzvp')
     self.assertEqual(level_3.auxiliary_basis, 'def2-tzvp/c')
     self.assertEqual(level_3.solvation_method, 'smd')
     self.assertEqual(level_3.solvent, 'water')
     self.assertIsInstance(level_3.solvation_scheme_level, Level)
     self.assertEqual(level_3.solvation_scheme_level.method, 'apfd')
     self.assertEqual(level_3.solvation_scheme_level.basis, 'def2-tzvp')
     self.assertEqual(
         str(level_3),
         "dlpno-ccsd(t)/def2-tzvp, auxiliary_basis: def2-tzvp/c, solvation_method: smd, "
         "solvent: water, solvation_scheme_level: 'apfd/def2-tzvp, software: gaussian (dft)', "
         "software: orca (wavefunction)")
Exemplo n.º 4
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 def test_lower(self):
     """Test the Level.lower() method"""
     level = Level(method='B3LYP',
                   basis='6-311+G(3df,2p)',
                   software='Gaussian',
                   dispersion='empiricaldispersion=Gd3bj',
                   solvation_method='SMD',
                   solvent='Water',
                   args={'KeyWord': 'IOP(99/33=1)'})
     self.assertEqual(level.method, 'b3lyp')
     self.assertEqual(level.basis, '6-311+g(3df,2p)')
     self.assertEqual(level.software, 'gaussian')
     self.assertEqual(level.dispersion, 'empiricaldispersion=gd3bj')
     self.assertEqual(level.solvation_method, 'smd')
     self.assertEqual(level.solvent, 'water')
     self.assertEqual(level.args, {
         'keyword': {
             'general': 'iop(99/33=1)'
         },
         'block': {}
     })
Exemplo n.º 5
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 def setUpClass(cls):
     """
     A method that is run before all unit tests in this class.
     """
     cls.maxDiff = None
     cls.ess_settings = {
         'gaussian': ['server1', 'server2'],
         'molpro': ['server2'],
         'qchem': ['server1'],
         'onedmin': ['server1'],
         'orca': ['server1'],
         'terachem': ['server1']
     }
     cls.xyz_c = {
         'symbols': ('C', ),
         'isotopes': (12, ),
         'coords': ((0.0, 0.0, 0.0), )
     }
     cls.job1 = Job(
         project='arc_project_for_testing_delete_after_usage3',
         ess_settings=cls.ess_settings,
         species_name='tst_spc',
         xyz=cls.xyz_c,
         job_type='opt',
         level=Level(repr={
             'method': 'b3lyp',
             'basis': '6-31+g(d)'
         }),
         multiplicity=1,
         fine=True,
         job_num=100,
         testing=True,
         project_directory=os.path.join(arc_path, 'Projects',
                                        'project_test'),
         initial_time=datetime.datetime(2019, 3, 15, 19, 53, 7, 0),
         final_time='2019-3-15 19:53:08',
     )
     cls.job1.determine_run_time()
Exemplo n.º 6
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def determine_scaling_factors(
    levels: List[Union[Level, dict, str]],
    ess_settings: Optional[dict] = None,
    init_log: Optional[bool] = True,
) -> list:
    """
    Determine the zero-point energy, harmonic frequencies, and fundamental frequencies scaling factors
    for a given frequencies level of theory.

    Args:
        levels (list): A list of frequencies levels of theory for which scaling factors are determined.
                       Entries are either Level instances, dictionaries, or simple string representations.
                       If a single entry is given, it will be converted to a list.
        ess_settings (dict, optional): A dictionary of available ESS (keys) and a corresponding server list (values).
        init_log (bool, optional): Whether to initialize the logger. ``True`` to initialize.
                                   Should be ``True`` when called as a standalone, but ``False`` when called within ARC.

    Returns:
        list: The determined frequency scaling factors.
    """
    if init_log:
        initialize_log(log_file='scaling_factor.log',
                       project='Scaling Factors')

    if not isinstance(levels, (list, tuple)):
        levels = [levels]
    levels = [
        Level(repr=level) if not isinstance(level, Level) else level
        for level in levels
    ]

    t0 = time.time()

    logger.info('\n\n\n')
    logger.info(HEADER)
    logger.info('\n\nstarting ARC...\n')

    # only run opt (fine) and freq
    job_types = initialize_job_types(
        dict())  # get the defaults, so no job type is missing
    job_types = {job_type: False for job_type in job_types.keys()}
    job_types['opt'], job_types['fine'], job_types['freq'] = True, True, True

    lambda_zpes, zpe_dicts, times = list(), list(), list()
    for level in levels:
        t1 = time.time()
        logger.info(
            f'\nComputing scaling factors at the {level} level of theory...\n\n'
        )
        renamed_level = rename_level(str(level))
        project = 'scaling_' + renamed_level
        project_directory = os.path.join(arc_path, 'Projects',
                                         'scaling_factors', project)
        if os.path.isdir(project_directory):
            shutil.rmtree(project_directory)

        species_list = get_species_list()

        if level.method_type == 'composite':
            freq_level = None
            composite_method = level
            job_types['freq'] = False
        else:
            freq_level = level
            composite_method = None

        ess_settings = check_ess_settings(ess_settings or global_ess_settings)

        Scheduler(project=project,
                  project_directory=project_directory,
                  species_list=species_list,
                  composite_method=composite_method,
                  opt_level=freq_level,
                  freq_level=freq_level,
                  ess_settings=ess_settings,
                  job_types=job_types,
                  allow_nonisomorphic_2d=True)

        zpe_dict = dict()
        for spc in species_list:
            zpe_dict[spc.label] = parse_zpe(
                os.path.join(project_directory, 'output', 'Species', spc.label,
                             'geometry',
                             'freq.out')) * 1000  # convert to J/mol
        zpe_dicts.append(zpe_dict)

        lambda_zpes.append(
            calculate_truhlar_scaling_factors(zpe_dict=zpe_dict,
                                              level=str(level)))
        times.append(time_lapse(t1))

    summarize_results(lambda_zpes=lambda_zpes,
                      levels=[str(level) for level in levels],
                      zpe_dicts=zpe_dicts,
                      times=times,
                      overall_time=time_lapse(t0))
    logger.info('\n\n\n')
    logger.info(HEADER)

    harmonic_freq_scaling_factors = [
        lambda_zpe * 1.014 for lambda_zpe in lambda_zpes
    ]
    return harmonic_freq_scaling_factors
Exemplo n.º 7
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    def setUpClass(cls):
        """
        A method that is run before all unit tests in this class.
        """
        cls.maxDiff = None
        cls.ess_settings = {
            'gaussian': ['server1'],
            'molpro': ['server2', 'server1'],
            'qchem': ['server1']
        }
        cls.project_directory = os.path.join(
            arc_path, 'Projects',
            'arc_project_for_testing_delete_after_usage3')
        cls.spc1 = ARCSpecies(label='methylamine', smiles='CN')
        cls.spc2 = ARCSpecies(label='C2H6', smiles='CC')
        xyz1 = """C       1.11424367   -0.01231165   -0.11493630
C      -0.07257945   -0.17830906   -0.16010022
O      -1.38500471   -0.36381519   -0.20928090
H       2.16904830    0.12689206   -0.07152274
H      -1.82570782    0.42754384   -0.56130718"""
        cls.spc3 = ARCSpecies(label='CtripCO', smiles='C#CO', xyz=xyz1)
        xyz2 = {
            'symbols': ('C', ),
            'isotopes': (12, ),
            'coords': ((0.0, 0.0, 0.0), )
        }
        cls.job1 = Job(project='project_test',
                       ess_settings=cls.ess_settings,
                       species_name='methylamine',
                       xyz=xyz2,
                       job_type='conformer',
                       conformer=0,
                       level={
                           'method': 'b97-d3',
                           'basis': '6-311+g(d,p)'
                       },
                       multiplicity=1,
                       project_directory=cls.project_directory,
                       job_num=101)
        cls.job2 = Job(project='project_test',
                       ess_settings=cls.ess_settings,
                       species_name='methylamine',
                       xyz=xyz2,
                       job_type='conformer',
                       conformer=1,
                       level={
                           'method': 'b97-d3',
                           'basis': '6-311+g(d,p)'
                       },
                       multiplicity=1,
                       project_directory=cls.project_directory,
                       job_num=102)
        cls.job3 = Job(project='project_test',
                       ess_settings=cls.ess_settings,
                       species_name='C2H6',
                       xyz=xyz2,
                       job_type='freq',
                       level={
                           'method': 'wb97x-d3',
                           'basis': '6-311+g(d,p)'
                       },
                       multiplicity=1,
                       project_directory=cls.project_directory,
                       software='qchem',
                       job_num=103)
        cls.rmg_database = rmgdb.make_rmg_database_object()
        cls.job_types1 = {
            'conformers': True,
            'opt': True,
            'fine_grid': False,
            'freq': True,
            'sp': True,
            'rotors': False,
            'orbitals': False,
            'lennard_jones': False,
        }
        cls.sched1 = Scheduler(
            project='project_test',
            ess_settings=cls.ess_settings,
            species_list=[cls.spc1, cls.spc2, cls.spc3],
            composite_method=None,
            conformer_level=Level(repr=default_levels_of_theory['conformer']),
            opt_level=Level(repr=default_levels_of_theory['opt']),
            freq_level=Level(repr=default_levels_of_theory['freq']),
            sp_level=Level(repr=default_levels_of_theory['sp']),
            scan_level=Level(repr=default_levels_of_theory['scan']),
            ts_guess_level=Level(repr=default_levels_of_theory['ts_guesses']),
            rmg_database=cls.rmg_database,
            project_directory=cls.project_directory,
            testing=True,
            job_types=cls.job_types1,
            orbitals_level=default_levels_of_theory['orbitals'],
            adaptive_levels=None,
        )
Exemplo n.º 8
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    def test_determine_adaptive_level(self):
        """Test the determine_adaptive_level() method"""
        # adaptive_levels get converted to ``Level`` objects in main, but here we skip main and test Scheduler directly
        adaptive_levels = {
            (1, 5): {
                ('opt', 'freq'): Level(repr='wb97xd/6-311+g(2d,2p)'),
                ('sp', ): Level(repr='ccsd(t)-f12/aug-cc-pvtz-f12')
            },
            (6, 15): {
                ('opt', 'freq'): Level(repr='b3lyp/cbsb7'),
                ('sp', ): Level(repr='dlpno-ccsd(t)/def2-tzvp')
            },
            (16, 30): {
                ('opt', 'freq'): Level(repr='b3lyp/6-31g(d,p)'),
                ('sp', ): Level(repr='wb97xd/6-311+g(2d,2p)')
            },
            (31, 'inf'): {
                ('opt', 'freq'): Level(repr='b3lyp/6-31g(d,p)'),
                ('sp', ): Level(repr='b3lyp/6-311+g(d,p)')
            }
        }

        sched2 = Scheduler(
            project='project_test',
            ess_settings=self.ess_settings,
            species_list=[self.spc1, self.spc2],
            composite_method=None,
            conformer_level=default_levels_of_theory['conformer'],
            opt_level=default_levels_of_theory['opt'],
            freq_level=default_levels_of_theory['freq'],
            sp_level=default_levels_of_theory['sp'],
            scan_level=default_levels_of_theory['scan'],
            ts_guess_level=default_levels_of_theory['ts_guesses'],
            rmg_database=self.rmg_database,
            project_directory=self.project_directory,
            testing=True,
            job_types=self.job_types1,
            orbitals_level=default_levels_of_theory['orbitals'],
            adaptive_levels=adaptive_levels)
        original_level = Level(method='CBS-QB3')
        level1 = sched2.determine_adaptive_level(
            original_level_of_theory=original_level,
            job_type='opt',
            heavy_atoms=5)
        level2 = sched2.determine_adaptive_level(
            original_level_of_theory=original_level,
            job_type='freq',
            heavy_atoms=5)
        level3 = sched2.determine_adaptive_level(
            original_level_of_theory=original_level,
            job_type='opt',
            heavy_atoms=20)
        level4 = sched2.determine_adaptive_level(
            original_level_of_theory=original_level,
            job_type='composite',
            heavy_atoms=50)
        level5 = sched2.determine_adaptive_level(
            original_level_of_theory=original_level,
            job_type='orbitals',
            heavy_atoms=5)
        level6 = sched2.determine_adaptive_level(
            original_level_of_theory=original_level,
            job_type='sp',
            heavy_atoms=7)
        level7 = sched2.determine_adaptive_level(
            original_level_of_theory=original_level,
            job_type='sp',
            heavy_atoms=25)
        self.assertEqual(level1.simple(), 'wb97xd/6-311+g(2d,2p)')
        self.assertEqual(level2.simple(), 'wb97xd/6-311+g(2d,2p)')
        self.assertEqual(level3.simple(), 'b3lyp/6-31g(d,p)')
        self.assertEqual(level4.simple(), 'cbs-qb3')
        self.assertEqual(level5.simple(), 'cbs-qb3')
        self.assertEqual(level6.simple(), 'dlpno-ccsd(t)/def2-tzvp')
        self.assertEqual(level7.simple(), 'wb97xd/6-311+g(2d,2p)')
Exemplo n.º 9
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    def test_conformers(self):
        """Test the parse_conformer_energy() and determine_most_stable_conformer() methods"""
        label = 'methylamine'
        self.job1.local_path_to_output_file = os.path.join(
            arc_path, 'arc', 'testing', 'methylamine_conformer_0.out')
        self.job1.job_status = [
            'done', {
                'status': 'done',
                'keywords': list(),
                'error': '',
                'line': ''
            }
        ]
        self.job2.local_path_to_output_file = os.path.join(
            arc_path, 'arc', 'testing', 'methylamine_conformer_1.out')
        self.job2.job_status = [
            'done', {
                'status': 'done',
                'keywords': list(),
                'error': '',
                'line': ''
            }
        ]
        self.sched1.job_dict[label] = dict()
        self.sched1.job_dict[label]['conformers'] = dict()
        self.sched1.job_dict[label]['conformers'][0] = self.job1
        self.sched1.job_dict[label]['conformers'][1] = self.job2
        self.sched1.species_dict[label].conformer_energies = [None, None]
        self.sched1.species_dict[label].conformers = [None, None]
        self.sched1.parse_conformer(job=self.job1, label=label, i=0)
        self.sched1.parse_conformer(job=self.job2, label=label, i=1)
        expecting = [-251596.4435088726, -254221.9433698632]
        self.assertAlmostEqual(
            self.sched1.species_dict[label].conformer_energies[0],
            expecting[0], 5)
        self.assertAlmostEqual(
            self.sched1.species_dict[label].conformer_energies[1],
            expecting[1], 5)
        self.sched1.species_dict[label].conformers[
            0] = parser.parse_xyz_from_file(
                self.job1.local_path_to_output_file)
        self.sched1.species_dict[label].conformers[
            1] = parser.parse_xyz_from_file(
                self.job2.local_path_to_output_file)

        self.sched1.determine_most_stable_conformer(label=label)
        expecting = {
            'symbols': ('N', 'C', 'H', 'H', 'H', 'H', 'H'),
            'isotopes': (14, 12, 1, 1, 1, 1, 1),
            'coords':
            ((-0.75555952, -0.12937106, 0.0), (0.7085544, 0.03887206, 0.0),
             (1.06395135, 1.08711266,
              0.0), (1.12732348, -0.45978507,
                     0.88433277), (1.12732348, -0.45978507, -0.88433277),
             (-1.16566701, 0.32023496, 0.81630508), (-1.16566701, 0.32023496,
                                                     -0.81630508))
        }
        self.assertTrue(
            almost_equal_coords_lists(
                self.sched1.species_dict[label].initial_xyz, expecting))
        methylamine_conf_path = os.path.join(
            self.sched1.project_directory, 'output', 'Species', 'methylamine',
            'geometry', 'conformers', 'conformers_after_optimization.txt')
        self.assertTrue(os.path.isfile(methylamine_conf_path))
        with open(methylamine_conf_path, 'r') as f:
            lines = f.readlines()
        self.assertTrue(
            'Conformers for methylamine, optimized at the wb97xd/def2svp level'
            in lines[0])
        self.assertEqual(lines[11], 'SMILES: CN\n')
        self.assertTrue('Relative Energy:' in lines[12])
        self.assertEqual(lines[16][0], 'N')

        self.sched1.output['C2H6'] = {
            'info': '',
            'paths': {
                'composite': '',
                'freq': '',
                'geo': ''
            },
            'isomorphism': '',
            'warnings': '',
            'errors': '',
            'job_types': {
                'opt': False,
                'composite': False,
                'sp': False,
                'fine_grid': False,
                'freq': False,
                'conformers': False
            },
            'convergence': True,
            'conformers': '',
            'restart': ''
        }
        self.sched1.run_conformer_jobs()
        save_conformers_file(project_directory=self.sched1.project_directory,
                             label='C2H6',
                             xyzs=self.sched1.species_dict['C2H6'].conformers,
                             level_of_theory=Level(method='CBS-QB3'),
                             multiplicity=1,
                             charge=0)
        c2h6_conf_path = os.path.join(self.sched1.project_directory, 'output',
                                      'Species', 'C2H6', 'geometry',
                                      'conformers',
                                      'conformers_before_optimization.txt')
        self.assertTrue(os.path.isfile(c2h6_conf_path))
        with open(c2h6_conf_path, 'r') as f:
            lines = f.readlines()
        self.assertEqual(lines[0], 'conformer 0:\n')
        self.assertEqual(lines[1][0], 'C')
        self.assertEqual(lines[9], '\n')
        self.assertEqual(lines[10], 'SMILES: CC\n')
Exemplo n.º 10
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"""
APIOxy levels module
used for storing default levels of theory
"""

from arc.level import Level


# Not implementing the "ML" and "0" levels

LEVELS = {1: {'sp_level': Level(method='b3lyp',
                                basis='6-31g(d,p)',
                                ),
              'opt_level': Level(method='b3lyp',
                                 basis='6-31g(d,p)',
                                 ),
              },
          2: {'sp_level': Level(method='wB97xd',
                                basis='def2TZVP',
                                solvation_method='SMD',
                                solvent='water',
                                ),
              'opt_level': Level(method='wB97xd',
                                 basis='def2SVP',
                                 ),
              },
          3: {'sp_level': Level(method='DLPNO',
                                basis='def2TZVP',
                                auxiliary_basis='def2TZVP/C',
                                args={'keyword': {'dlpno_threshold': 'normalPNO'}},
                                # solvation_method='COSMO/tzvpd-fine',
Exemplo n.º 11
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 def test_deduce_software(self):
     """Test deducing an ESS by the level"""
     self.assertEqual(
         Level(method='B3LYP', basis='6-311g+(d,f)').software, 'gaussian')
     level_1 = Level(method='B3LYP/6-311g+(d,f)')
     level_1.deduce_software(job_type='onedmin')
     self.assertEqual(level_1.software, 'onedmin')
     self.assertEqual(
         Level(method='b3lyp', basis='6-311g+(d,f)').software, 'gaussian')
     level_2 = Level(method='b3lyp', basis='6-311g+(d,f)')
     level_2.deduce_software(job_type='orbitals')
     self.assertEqual(level_2.software, 'qchem')
     self.assertEqual(
         Level(method='B3LYP', basis='6-311g+(d,f)').software, 'gaussian')
     level_3 = Level(method='B3LYP', basis='6-311g+(d,f)')
     level_3.deduce_software(job_type='irc')
     self.assertEqual(level_3.software, 'gaussian')
     self.assertEqual(
         Level(method='DLPNO-CCSD(T)', basis='def2-tzvp').software, 'orca')
     self.assertEqual(Level(method='PM6').software, 'gaussian')
     self.assertEqual(Level(method='HF').software, 'gaussian')
     self.assertEqual(
         Level(method='CCSD(T)-F12', basis='aug-cc-pVTZ').software,
         'molpro')
     self.assertEqual(
         Level(method='CISD', basis='aug-cc-pVTZ').software, 'molpro')
     self.assertEqual(
         Level(method='b3lyp', basis='6-311g+(d,f)').software, 'gaussian')
     self.assertEqual(
         Level(method='wb97x-d', basis='def2-tzvp').software, 'qchem')
     self.assertEqual(
         Level(method='wb97xd', basis='def2-tzvp').software, 'gaussian')
     self.assertEqual(
         Level(method='b97', basis='def2-tzvp').software, 'gaussian')
     self.assertEqual(
         Level(method='m06-2x', basis='def2-tzvp').software, 'qchem')
     self.assertEqual(
         Level(method='m062x', basis='def2-tzvp').software, 'gaussian')
     self.assertEqual(
         Level(method='b3p86', basis='6-311g+(d,f)').software, 'terachem')
     self.assertEqual(
         Level(method='new',
               basis='new',
               args={
                   'keywords': {
                       'general': 'iop(99/33=1)'
                   }
               }).software, 'gaussian')
Exemplo n.º 12
0
 def test_copy(self):
     """Test copying the object"""
     level_1 = Level(repr='wB97xd/def2-tzvp')
     level_2 = level_1.copy()
     self.assertIsNot(level_1, level_2)
     self.assertEqual(level_1.as_dict(), level_2.as_dict())
Exemplo n.º 13
0
 def test_to_arkane(self):
     """Test converting Level to LevelOfTheory"""
     level_1 = Level(repr='wB97xd/def2-tzvp')
     self.assertEqual(
         level_1.to_arkane_level_of_theory(),
         LevelOfTheory(method='wb97xd',
                       basis='def2tzvp',
                       software='gaussian'))
     self.assertEqual(
         level_1.to_arkane_level_of_theory(variant='freq'),
         LevelOfTheory(method='wb97xd',
                       basis='def2tzvp',
                       software='gaussian'))
     level_2 = Level(repr='CBS-QB3')
     self.assertEqual(level_2.to_arkane_level_of_theory(),
                      LevelOfTheory(method='cbs-qb3', software='gaussian'))
     self.assertEqual(level_2.to_arkane_level_of_theory(variant='AEC'),
                      LevelOfTheory(method='cbs-qb3', software='gaussian'))
     self.assertEqual(level_2.to_arkane_level_of_theory(variant='freq'),
                      LevelOfTheory(method='cbs-qb3', software='gaussian'))
     self.assertEqual(level_2.to_arkane_level_of_theory(variant='BAC'),
                      LevelOfTheory(method='cbs-qb3', software='gaussian'))
     self.assertIsNone(
         level_2.to_arkane_level_of_theory(
             variant='BAC', bac_type='m'))  # might change in the future
     level_3 = Level(
         repr={
             'method': 'DLPNO-CCSD(T)',
             'basis': 'def2-TZVp',
             'auxiliary_basis': 'def2-tzvp/c',
             'solvation_method': 'SMD',
             'solvent': 'water',
             'solvation_scheme_level': 'APFD/def2-TZVp'
         })
     self.assertEqual(
         level_3.to_arkane_level_of_theory(),
         LevelOfTheory(method='dlpno-ccsd(t)',
                       basis='def2tzvp',
                       software='orca'))
     self.assertEqual(
         level_3.to_arkane_level_of_theory(comprehensive=True),
         LevelOfTheory(method='dlpnoccsd(t)',
                       basis='def2tzvp',
                       auxiliary_basis='def2tzvp/c',
                       solvent='water',
                       solvation_method='smd',
                       software='orca'))